MOLECULAR-DYNAMICS ANALYSIS OF A RIBONUCLEASE C-PEPTIDE ANALOG

We have carried out a nanosecond molecular dynamics simulation of an a nalogue of the ribonuclease C-peptide in water. The overall conformati on has an extended region for the first three amino acids connected to an a-helix for residues 4-13, and this basic structure is preserved t hroughout the simulation, with helical hydrogen bonds present 87% of t he time, on average. The final helical hydrogen bond is spontaneously broken and re-formed several times, providing a detailed picture of su ch winding/unwinding events. The simulation was used to estimate the e ffects of internal motion on proton nuclear Overhauser effect spectros copy (NOESY) intensities for several classes of important cross peaks. Within the helical regions, the effects of internal motion vary only a little from one residue to another for backbone-backbone cross peaks , and the relevant correlation functions reach plateau values within a bout 50 ps. The spectral simulations show, however, that it may be dif ficult to establish a close quantitative connection between NOESY cros s-peak volumes and measures of helical content. (C) 1993 John Wiley & Sons, Inc.